FOXN1 p.Pro416fs
c.1247del · rs1567886959 · VCV598960
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 8 of 9 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.87 | GERP -0.78, phastCons 0.98 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- FOXN1
- Protein
- p.Pro416fs
- Coding
- c.1247del
- MANE Select
- NM_001369369
- dbSNP
- rs1567886959
- Type
- Deletion
- Location
- chr17:28534814 (GRCh38)
- Gene constraint
- LOEUF 0.442 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.44 · 2 PDB
- Residue 416
- a UniProt-annotated variant site (in tidand and tlind); the 'disordered' region
Disease context
Similar variants
- FOXN1 p.Asn349fs Likely pathogenic ★★ same condition
- FOXN1 p.Leu413fs Pathogenic/Likely pathogenic ★★ same condition
- FOXN1 p.Leu536fs Likely pathogenic ★ same condition
- FOXN1 p.Pro416= Likely benign ★ same residue
- FOXN1 p.Trp180Ter Likely pathogenic ★ same condition
- FOXN1 p.Gly146Glu Uncertain significance ★ ⚠ same condition
- FOXN1 p.Thr567Lys Uncertain significance ★ ⚠ same condition
- FOXN1 p.Glu303fs Likely pathogenic ★★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/foxn1-p-pro416fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown